VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Wed Apr 09 2008 - 03:06:08 CDT

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Hi!

Subramanian Vaitheeswaran wrote:
> The system I am simulating consists of two small
> solute molecules in a cubic water box.
> I want to wrap the coords in the dcd trajectory
> so that the nearest images of the solutes are displayed,
> using the usual minimum image convention.
>
> "pbc join" in PBCTools ver. 2.1 looks like it might do the job.

I do not completely understand what you mean when you state that "the
nearest image" is to be displayed. The nearest image to what?

In any case, "pbc join" is most probably the wrong tool for your job. It
can be used to (re)join compounds that have been wrapped previously, but
it won't (re)wrap.

What you probably need is "pbc wrap", that you can use to wrap all atoms
into a single unit cell that has its center at the specified position,
i.e. it will display the minimum image of all atoms to this position.
Please read the documentation of "pbc wrap" to learn about all its options:

        http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Olaf
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